HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS

Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, and HERV-K, remaining active for transposition. Along with other types of genomic variants, retrotransponson-derived variants contribute to the whole spectrum of genome variants in humans. With the advancement of sequencing techniques, many human genomes are being sequenced at the individual level, fueling the comparative research on these variants among individuals. In this thesis, the evolution and functional impact of structural variations is examined primarily focusing on retrotransposons in the context of human evolution. The thesis comprises of three different studies on the topics that are presented in three data chapters. First, the recent evolution of all human specific AluYb members, representing the second most active subfamily of Alus, was tracked to identify their source/master copy using a novel approach. All human-specific AluYb elements from the reference genome were extracted, aligned with one another to construct clusters of similar copies and each cluster was analyzed to generate the evolutionary relationship between the members of the cluster. The approach resulted in identification of one major driver copy of all human specific Yb8 and the source copy of the Yb9 lineage. Three new subfamilies within the AluYb family – Yb8a1, Yb10 and Yb11 were also identified, with Yb11 being the youngest and most polymorphic. Second, an attempt to construct a relation between transposable elements (TEs) and tandem repeats (TRs) was made at a genome-wide scale for the first time. Upon sequence comparison, positional cross-checking and other relevant analyses, it was observed that over 20% of all TRs are derived from TEs. This result established the first connection between these two types of repetitive elements, and extends our appreciation for the impact of TEs on genomes. Furthermore, only 6% of these TE-derived TRs follow the already postulated initiation and expansion mechanisms, suggesting that the others are likely to follow a yet-unidentified mechanism. Third, by taking a combination of multiple computational approaches involving all types of genetic variations published so far including transposable elements, the first whole genome sequence of the most recent common ancestor of all modern human populations that diverged into different populations around 125,000-100,000 years ago was constructed. The study shows that the current reference genome sequence is 8.89 million base pairs larger than our common ancestor’s genome, contributed by a whole spectrum of genetic mechanisms. The use of this ancestral reference genome to facilitate the analysis of personal genomes was demonstrated using an example genome and more insightful recent evolutionary analyses involving the Neanderthal genome. The three data chapters presented in this thesis conclude that the tandem repeats and transposable elements are not two entirely distinctly isolated elements as over 20% TRs are actually derived from TEs. Certain subfamilies of TEs themselves are still evolving with the generation of newer subfamilies. The evolutionary analyses of all TEs along with other genomic variants helped to construct the genome sequence of the most recent common ancestor to all modern human populations which provides a better alternative to human reference genome and can be a useful resource for the study of personal genomics, population genetics, human and primate evolution.

Avaliação dos produtos da degradação oxidativa da Hb S nos genótipos SS, SF (S/beta0 talassemia) e AS, em comparação com hemoglobinas normais

A doença falciforme é um termo genérico usado para determinar um grupo de alterações genéticas caracterizadas pelo predomínio de hemoglobina (Hb) S. Os principais genótipos que compõem o grupo de doença falciforme são os seguintes: SS, SF [S/beta0 talassemia e S/persistência hereditária de Hb fetal (PHHF)], SFA (S/beta+ talassemia), SC, SD e SH (S/alfa talassemia). O presente trabalho analisa os resultados das avaliações de produtos provenientes da oxidação da Hb S, identificados pela concentração da metemoglobina e de eritrócitos com corpos de Heinz em dois genótipos da doença falciforme (SS e S/beta0 talassemia) e no traço falcêmico (AS), em comparação com o genótipo normal (AA). A análise dos produtos da degradação oxidativa da hemoglobina, evidenciados pelo aumento dos valores das médias referentes à concentração de metemoglobina e do número de eritrócitos com corpos de Heinz, está diretamente relacionada com o aumento da concentração da Hb S. Assim, a degradação oxidativa da hemoglobina decresce entre os genótipos estudados da seguinte forma: SS>SF>AS>AA. É importante destacar que as análises indicaram que a simples presença de Hb S no eritrócito, como é o caso do genótipo AS, é capaz de causar elevação da concentração de metemoglobina em 52,62% das amostras analisadas e de induzir a precipitação de corpos de Heinz em 73,68% dos casos estudados. Explicações referentes aos processos oxidativos e redutores das hemoglobinas estudadas são apresentados no texto. Destaca-se, entre os resultados apresentados, a identificação por meio de eletroforese em agarose alcalina da fração de globina alfa-livre em todas as amostras do genótipo SF provenientes de pessoas com Hb S/beta0 talassemia. É proposto um esquema para explicar a origem da globina alfa-livre, especialmente para o genótipo S/beta0 talassemia, e a importância da sua identificação no diagnóstico laboratorial de Hb S/beta0 talassemia.

Abnormal hemoglobin phenotypes in carriers of mild anemia in Latin America.

We looked for abnormal hemoglobins in blood samples sent for diagnosis of anemia. Identification of the hemoglobins was made using electrophoretic, chromatographic and molecular procedures. The 2020 blood samples were of patients from various regions of Brazil and from some other Latin American countries. Among the abnormal hemoglobins that we found, 3.5% are known to be rare, while 51% had an electrophoretic profile similar to that of Hb S at alkaline pH. Differentiation was possible only by combining electrophoretic and chromatographic methods. Hb Hasharon, an alpha globin chain mutant, was the most frequently found variant hemoglobin; it accounted for 14.3% of the abnormal DNA samples. The other abnormal hemoglobin phenotypes displayed distinct electrophoretic profiles; most of them migrated faster than Hb A. The frequencies of the different abnormal hemoglobin profiles that we found reflect the miscegenation of the Latin American population and indicate the importance of hemoglobin studies using various methods in combination for accurate diagnosis and appropriate counseling of carriers and their families.

Influence of δβ-thalassemia or regulatory elements in individuals with increased fetal Hb levels in the São Paulo northwest population

Fetal hemoglobin (Hb F), formed by two alpha globin chains (α) and two gamma chains (γ) (α2 γ2), has reduced expression in adults, ranging from 0 to 1% of total hemoglobin. Increased levels of Hb F are due to mutations in the β-globin family, which cause hereditary persistence of fetal hemoglobin (HPFH) and delta-beta thalassemia (δβ-thalassemia).The control of the production takes place by the regulatory region and regions outside the β-globin family, among them 2q16, 6q23, 8q, and Xp22.2.The aims of this study were to determine the presence and frequency of two mutations for δβ-thalassemia, the XmnI polymorphism and β-globin haplotypes in healthy individuals with increased Hb F in the State of São Paulo. We analyzed 60 samples of peripheral blood of healthy adults, without complaints of anemia. The samples were separated into two groups according to Hb F level: group I - 34 samples with Hb F ranging from 2 to 15% and group II - 26 samples with Hb F over 15%. In relation to the polymorphisms examined, we found three heterozygous individuals (5%) for Spanish δβ-thalassemia, belonging to group I, whose Hb F levels were within the normal range.The Sicilian δβ-thalassemia mutation was not found, indicating the need to study other polymorphisms related to the increase of Hb F in adult life.The frequency of XmnI polymorphism was 33.3% and the mean Hb F levels were 15.48 ± 11.69%.The frequency observed in our study for this polymorphic site is higher than that found in the literature for healthy subjects.This polymorphism was more prevalent in individuals with Hb F levels below 15%. For four samples positive for this polymorphism, the Hb F levels were explained by the presence of HPFH and Spanish δβ-thalassemia mutations, so that the presence of the XmnI polymorphic site was not a determinant in the overexpression of γ-globin genes. Regarding β-globin haplotypes, 18 alleles and 27 distinct genotypic patterns were found.The pattern Atp1/Atp2 was the mostfrequent genotype (13.72%).Of the 18 alleles, 13 showed atypical patterns.The results show that the haplotype V was the most frequent (27.45%), followed by atypical Atp2 (13.72%) and Atp1 (11.76%), and that there was a higher correlation with the presence of HPFH and XmnI polymorphism.The high frequency of haplotype V in our samples and high frequency of atypical haplotypes may reflect a high rate of miscegenation in this population, suggesting an ethnic characteristic for the Brazilian population, requiring the evaluation of population genetic markers to corroborate this hypothesis. © FUNPEC-RP.

Influência da δβ-Talassemia ou de elementos de regulação em indivíduos com hemoglobina fetal aumentada na população da região Noroeste do Estado de São Paulo

Pós-graduação em Genética - IBILCE

Imobilização de fosfatos em microesferas poliméricas contendo biochar: preparação, caracterização e liberação lenta em sistemas aquosos

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Identification of CNV and QTL for productive and functional traits in dairy cattle using dense SNP chips

The thesis identify CNV structural variants as possible markers for genomic selection and identify QTL regions for Fatty Acid Content in the Italian Brown Swiss population. Additionally it maps the QTL for mastitis resistance in the Valdostana Red Pied cattle.

Bedeutung von allelen Varianten des Hexose-Transporters Hxt3p und der Hexokinasen Hxk1p und Hxk2p für Aufnahme und Verwertung von Glucose und Fructose durch Weinhefen

In Hinsicht darauf, dass sich S. cerevisiae-Stämme im Laufe der Domestizierung und Anpassung an verschiedene Habitate genetisch verändert haben, wurde in dieser Arbeit eine repräsentative Auswahl von Labor-, kommerziellen und in der Natur vorkommenden Saccharomyces-Stämmen und ihren Interspezies-Hybriden auf die Verbreitung alleler Varianten der Hexokinase-Gene HXK1 und HXK2 getestet. Von den Hexose-Transportern stand Hxt3p im Mittelpunkt, da seine essentielle Rolle bei der Vergärung von Glucose und Fructose bereits belegt wurde.rnIn dieser Arbeit wurde gezeigt, dass es bedeutende Unterschiede in der Vergärung von Glucose und Fructose zwischen Weinhefen der Gattung Saccharomyces gibt, die z.T. mit Struktur-Varianten des Hexose-Transporter Hxt3p korrelieren. rnInsgesamt 51 Hefestämme wurden auf ihre allele Variante des HXT3-Gens untersucht. Dabei haben sich drei Hauptgruppen (die Fermichamp®-Typ Gruppe, Bierhefen und Hybrid-Stämme) mit unterschiedlichem HXT3-Allel ergeben. Im Zusammenhang mit der Weinherstellung wurden signifikante Nukleotid-Substitutionen innerhalb des HXT3-Gens der robusten S. cerevisiae-Stämme (wie z.B. Sekthefen, kommerzielle Starterkulturen) und Hybrid-Stämmen festgestellt. Diese Hefen zeichneten sich durch die Fähigkeit aus, den Most trotz stressigen Umwelt-Bedingungen (wie hohe Ethanol-Konzentration, reduzierter Ammonium-Gehalt, ungünstiges Glucose:Fructose-Verhältnis) zu vergären. rnDie Experimente deuten darauf hin, dass die HXT3-Allel-Variante des als Starterkultur verwendbaren Stammes Fermichamp®, für den verstärkten Fructose-Abbau verantwortlich ist. Ein gleiches Verhalten der Stämme mit dieser Allel-Variante wurde ebenfalls beobachtet. Getestet wurden die S. cerevisiae-Stämme Fermichamp® und 54.41, die bezüglich Hxt3p-Aminosäuresequenz gleich sind, gegenüber zwei S. cerevisiae-Stämmen mit dem HXT3-Standard-Alleltyp Fermivin® und 33. Der Unterschied in der Hexose-Verwertung zwischen Stämmen mit Fermichamp®- und Standard-Alleltyp war in der Mitte des Gärverlaufs am deutlichsten zu beobachten. Beide Gruppen, sowohl mit HXT3 Fermichamp®- als auch Fermivin®-Alleltyp vergoren die Glucose schneller als die Fructose. Der Unterschied aber zwischen diesen HXT3-Alleltypen bei der Zucker-Verwertung lag darin, dass der Fermichamp®-Typ eine kleinere Differenz in der Abbau-Geschwindigkeit der beiden Hexosen zeigte als der Fermivin®-Typ. Die Zuckeraufnahme-Messungen haben die relativ gute Fructose-Aufnahme dieser Stämme bestätigt.rnEbenfalls korrelierte der fructophile Charakter des Triple-Hybrides S. cerevisiae x S. kudriavzevii x S. bayanus-Stamm HL78 in Transportexperimenten mit verstärkter Aufnahme von Fructose im Vergleich zu Glucose. Insgesamt zeigte dieser Stamm ähnliches Verhalten wie die S. cerevisiae-Stämme Fermichamp® und 54.41. rnIn dieser Arbeit wurde ein Struktur-Modell des Hexose-Transporters Hxt3p erstellt. Als Basis diente die zu 30 % homologe Struktur des Proton/Xylose-Symporters XylE aus Escherichia coli. Anhand des Hxt3p-Modells konnten Sequenzbereiche mit hoher Variabilität (Hotspots) in drei Hxt3p-Isoformen der Hauptgruppen (die Fermichamp®-Typ Gruppe, Bierhefen und Hybrid-Stämme) detektiert werden. Diese signifikanten Aminosäure-Substitutionen, die eine mögliche Veränderung der physikalischen und chemischen Eigenschaften des Carriers mit sich bringen, konzentrieren sich auf drei Bereiche. Dazu gehören die Region zwischen den N- und C-terminalen Domänen, die cytosolische Domäne und der Outside-Loop zwischen Transmembranregion 9 und Transmembranregion 10. rnObwohl die Transportmessungen keinen Zusammenhang zwischen Stämmen mit unterschiedlichen HXT3-Allelen und ihrer Toleranz gegenüber Ethanol ergaben, wurde ein signifikanter Anstieg in der Zuckeraufnahme nach vorheriger 24-stündiger Inkubation mit 4 Vol% Ethanol bei den Teststämmen beobachtet. rnInsgesamt könnten allele Varianten von HXT3-Gen ein nützliches Kriterium bei der Suche nach robusten Hefen für die Weinherstellung oder für andere industrielle Anwendungen sein. Die Auswirkung dieser Modifikationen auf die Struktur und Effizienz des Hexose-Transporters, sowie der mögliche Zusammenhang mit Ethanol-Resistenz müssen weiter ausführlich untersucht werden. rnEin Zusammenhang zwischen den niedrig variablen Allel-Varianten der Hexokinase-Gene HXK1 und HXK2 und dem Zucker-Metabolismus wurde nicht gefunden. Die Hexokinasen der untersuchten Stämme wiesen allerdings generell eine signifikante geringere Affinität zu Fructose im Vergleich zu Glucose auf. Hier liegt sicherlich eine Hauptursache für den Anstieg des Fructose:Glucose-Verhältnisses im Laufe der Vergärung von Traubenmosten.rn

New insights into the performance of human whole-exome capture platforms.

Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most recent standard exome enrichment platforms from Agilent, NimbleGen and Illumina applied to six different DNA samples by two sequencing vendors per platform. Our results suggest that both Agilent and NimbleGen overall perform better than Illumina and that the high enrichment performance of Agilent is stable among samples and between vendors, whereas NimbleGen is only able to achieve vendor- and sample-specific best exome coverage. Moreover, the recent Agilent platform overall captures more coding exons with sufficient read depth than NimbleGen and Illumina. Due to considerable gaps in effective exome coverage, however, the three platforms cannot capture all known coding exons alone or in combination, requiring improvement. Our data emphasize the importance of evaluation of updated platform versions and suggest that enrichment-free whole genome sequencing can overcome the limitations of WES in sufficiently covering coding exons, especially GC-rich regions, and in characterizing structural variants.

The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability

The crystal and molecular structure of an RNA duplex corresponding to the high affinity Rev protein binding element (RBE) has been determined at 2.1-Å resolution. Four unique duplexes are present in the crystal, comprising two structural variants. In each duplex, the RNA double helix consists of an annealed 12-mer and 14-mer that form an asymmetric internal loop consisting of G-G and G-A noncanonical base pairs and a flipped-out uridine. The 12-mer strand has an A-form conformation, whereas the 14-mer strand is distorted to accommodate the bulges and noncanonical base pairing. In contrast to the NMR model of the unbound RBE, an asymmetric G-G pair with N2-N7 and N1-O6 hydrogen bonding, is formed in each helix. The G-A base pairing agrees with the NMR structure in one structural variant, but forms a novel water-mediated pair in the other. A backbone flip and reorientation of the G-G base pair is required to assume the RBE conformation present in the NMR model of the complex between the RBE and the Rev peptide.

Novel tear film supplements:a potential application for synthetic protein-phospholipid complexes

Purpose: Surfactant proteins A, B, C and D complex with (phospho)lipids to produce surfactants which provide low interfacial tensions. It is likely that similar complexation occurs in the tear film and contributes to its low surface tension. Synthetic protein-phospholipid complexes, with styrene maleic anhydrides (SMAs) as the protein analogue, have been shown to have similarly low surface tensions. This study investigates the potential of modified SMAs and/or SMA-phospholipid complexes, which form under physiological conditions, to supplement natural tear film surfactants. Method: SMAs were modified to provide structural variants which can form complexes under varying conditions. Infrared spectroscopy and Nuclear Magnetic Resonance were used to confirm SMA structure. Interfacial behaviour of the SMA and SMA-phospholipid complexes was studied using Langmuir trough, du Nûoy ring and pulsating bubblemethods. Factors which affect SMA-phospholipid complex formation, such as temperature and pH, were also investigated. Results: Structural manipulation of SMAs allows control over complex formation, including under physiological conditions (e.g. partial SMAesterfication allowed complexation with dimyristoylphosphatidylcholine, at pH7). The low surface tensions of the SMAs (42mN/m for static (du Nûoy ring) and 34mN/m for dynamic (Langmuir) techniques) demonstrate their surface activity at the air-aqueous interface. SMA-phospholipid complexes provide even lower surface tensions (~2 mN/m), approaching that of lung surfactant, as measured by the pulsating bubblemethod. Conclusions: Design of the molecular architecture of SMAs allows control over their surfactant properties. These SMAs could be used as novel tear films supplements, either alone to complex with native tear film phospholipids or delivered as synthetic protein-phospholipid complexes.

Making political films politically?:the film-making practice of Jean-Luc Godard

This thesis attempts to re-examine the work of Jean-Luc Godard and in particular the claims which have been made for it as the starting-point for a revolutionary cinema.This re-examination involves, firstly, a critical summary of the development of Structuralist thinking, from its origins in linguistics, with Saussure, through to its influence on Marxism, with Althusser. It is this `Structural Marxism' which prepared the ground for a view of Godard as a revolutionary film-maker so its influences on film theory in the decade after 1968 is traced in journals such as Cahiers du Cinéma and Screen and in the work of their editors and contributors. Godard's relationship with such theories was a complex one and some of the cross-breeding is revealed in a brief account of his own ideas about his film-making. More important, however is his practice as a committed `political' film-maker between 1968 and 1972 which is analysed in terms of the responses it makes to the cultural opportunities offered in the period after the revolutionary situation of May 1968. The severe problems revealed by that analysis may be partially resolved in Godard's greatest `political' achievement Tout va bien, but a comparative analysis proves that in earlier `a-political' films such as Vivre sa vie, he was creating more meaningful and perhaps even more revolutionary art, whose formal experimentation is more organically linked to its subject and whose ability to communicate ideas far oustrips the later work. In conclusion some indications are suggested of a more fruitful basis for Marxist theories of art than Structural variants, seeking a non-formalist approach in the work of Marx, of Trotsky, of Brecht and Lukacs.

Avaliação do potencial cancerigénico de microcistinas (cianotoxinas)

Tese de doutoramento em Farmácia (Toxicologia), apresentada à Faculdade de Farmácia da Universidade de Lisboa, 2009.

Structural and functional studies of the human integrin $\alpha 4\beta 1$ (CD49d/CD29)

The integrin receptor $\alpha 4\beta 1$ is a cell surface heterodimer involved in a variety of highly regulated cellular interactions. The purpose of this dissertation was to identify and characterize unique structural and functional properties of the $\alpha 4\beta 1$ molecule that may be important for adhesion regulation and signal transduction. To study these properties and to establish a consensus sequence for the $\alpha 4$ subunit, cDNA encoding $\alpha 4$ was cloned and sequenced. A comparison with previously described human $\alpha 4$ sequences identified several substitutions in the $5\prime$ and $3\prime$ untranslated regions, and a nonsynonymous G to A transition in the coding region, resulting in a glutamine substitution for arginine. Further analysis of this single nucleotide substitution indicated that two variants of the $\alpha 4$ subunit exist, and when compared with three ancestrally-related species, the new form cloned in our laboratory was found to be evolutionarily conserved.^ The expression of $\alpha 4$ cDNA in transfected K562 erythroleukemia cells, and subsequent studies using flow cytofluorometric, immunochemical, and ligand binding/blocking analyses, confirmed $\alpha 4\beta 1$ as a receptor for fibronectin (FN) and vascular cell adhesion molecule-1 (VCAM-1), and provided a practical means of identifying two novel monoclonal antibody (mAb) binding epitopes on the $\alpha 4\beta 1$ complex that may play important roles in the regulation of leukocyte adhesion.^ To investigate the association of $\alpha 4\beta 1$-mediated adhesion with signals involved in the spreading of lymphocytes on FN, a quantitative method of analysis was developed using video microscopy and digital imaging. The results showed that HPB-ALL $(\alpha 4\beta 1\sp{\rm hi},\ \alpha 5\beta 1\sp-)$ cells could adhere and actively spread on human plasma FN, but not on control substrate. Many cell types which express different levels of the $\alpha 4\beta 1$ and $\alpha 5\beta 1$ FN binding integrins were examined for their ability to function in these events. Using anti-$\alpha 4$ and anti-$\alpha 5$ mAbs, it was determined that cell adhesion to FN was influenced by both $\beta 1$ integrins, while cell spreading was found to be dependent on the $\alpha 4\beta 1$ complex. In addition, inhibitors of phospholipase A$\sb2$ (PLA$\sb2$), 5-lipoxygenases, and cyclooxygenases blocked HPB-ALL cell spreading, yet had no effect on cell adhesion to FN, and the impaired spreading induced by the PLA$\sb2$ inhibitor cibacron blue was restored by the addition of exogenous arachidonic acid (AA). These results suggest that the interaction of $\alpha 4\beta 1$ with FN, the activation of PLA$\sb2,$ and the subsequent release of AA, may be involved in lymphocyte spreading. ^

Structural and functional characterization of the conserved salt bridge in mammalian Paneth cell alpha-defensins - Solution structures of mouse cryptdin-4 AND (E15D)-cryptdin-4

Defensins are mediators of mammalian innate immunity, and knowledge of their structure-function relationships is essential for understanding their mechanisms of action. We report here the NMR solution structures of the mouse Paneth cell α-defensin cryptdin-4 (Crp4) and a mutant (E15D)-Crp4 peptide, in which a conserved Glu15 residue was replaced by Asp. Structural analysis of the two peptides confirms the involvement of this Glu in a conserved salt bridge that is removed in the mutant because of the shortened side chain. Despite disruption of this structural feature, the peptide variant retains a well defined native fold because of a rearrangement of side chains, which result in compensating favorable interactions. Furthermore, salt bridge-deficient Crp4 mutants were tested for bactericidal effects and resistance to proteolytic degradation, and all of the variants had similar bactericidal activities and stability to proteolysis. These findings support the conclusion that the function of the conserved salt bridge in Crp4 is not linked to bactericidal activity or proteolytic stability of the mature peptide.